WIP fix #1330

cwltool/command_line_tool.py

@@ -201,6 +201,24 @@ def job(
     ) -> Generator[ExpressionJob, None, None]:
         builder = self._init_job(job_order, runtimeContext)
 
+        paramskey = []
+        paramskeys = []
+
+        if self.tool["inputs"] is not None:
+            for inp in self.tool["inputs"]:
+                for k, v in inp.items():
+                    if k == "id":
+                        paramskey.append(v)
+                        paramskeys.append(shortname(v))
+        if builder.job is not None:
+            newbj = {}
+            for k, v in dict(builder.job).items():
+                if k in paramskey:
+                    newbj[k] = v
+                elif k in paramskeys:
+                    newbj[k] = v
+            builder.job = newbj
+
         job = ExpressionJob(
             builder,
             self.tool["expression"],
@@ -989,6 +1007,23 @@ def update_status_output_callback(
 
         builder = self._init_job(job_order, runtimeContext)
 
+        paramskey = []
+        paramskeys = []
+
+        if self.tool["inputs"] is not None:
+            for inp in self.tool["inputs"]:
+                for k, v in inp.items():
+                    if k == "id":
+                        paramskey.append(v)
+                        paramskeys.append(shortname(v))
+        if builder.job is not None:
+            newbj = {}
+            for k, v in dict(builder.job).items():
+                if k in paramskey:
+                    newbj[k] = v
+                elif k in paramskeys:
+                    newbj[k] = v
+            builder.job = newbj
         reffiles = copy.deepcopy(builder.files)
 
         j = self.make_job_runner(runtimeContext)(

cwltool/schemas/v1.1/conformance_tests.yaml

@@ -2598,6 +2598,17 @@
   doc: Test an anonymous enum inside an array inside a record, SchemaDefRequirement
   tags: [command_line_tool, schema_def]
 
+
+- job: tests/empty.json
+  tool: tests/fail-unconnected-expressiontool.cwl
+  label: wf_step_access_undeclared_param_expressiontool
+  id: 198
+  doc: >-
+    Test that parameters that don't appear in the `run` process
+    inputs are not present in the input object used to run the expressiontool.
+  should_fail: true
+  tags: [ required, workflow ]
+
 # New tests for v1.1
 
 - job: tests/wc-job.json

cwltool/workflow.py

@@ -452,7 +452,13 @@ def job(
             field = shortname(inp["id"])
             if not inp.get("not_connected"):
                 step_input[field] = job_order[inp["id"]]
-
+        for inp in dict(job_order).keys():
+            field = shortname(inp)
+            step_input[field] = job_order[inp]
+            # if not isinstance(inp, str):
+            #     if hasattr(inp, "get"):
+            #    if not inp.get("not_connected"):
+            #        step_input[field] = job_order[field]
         try:
             yield from self.embedded_tool.job(
                 step_input,

cwltool/workflow_job.py

@@ -386,6 +386,12 @@ def object_from_state(
     incomplete: bool = False,
 ) -> Optional[CWLObjectType]:
     inputobj = {}  # type: CWLObjectType
+    if state is not None:
+        for s in state.keys():
+            ss = state[s]
+            if ss is not None:
+                if isinstance(ss, WorkflowStateItem):
+                    inputobj[s] = ss.value
     for inp in params:
         iid = original_id = cast(str, inp["id"])
         if frag_only:
@@ -551,6 +557,24 @@ def do_output_callback(self, final_output_callback: OutputCallbackType) -> None:
             _logger.debug("[%s] outputs %s", self.name, json_dumps(wo, indent=4))
 
         self.did_callback = True
+        paramskey = []
+        paramskeys = []
+
+        if self.tool["outputs"] is not None:
+            for inp in self.tool["outputs"]:
+                for k, v in inp.items():
+                    if k == "id":
+                        paramskey.append(v)
+                        paramskeys.append(shortname(v))
+
+        if wo is not None:
+            newwo = {}
+            for k, v in dict(wo).items():
+                if k in paramskey:
+                    newwo[k] = v
+                elif k in paramskeys:
+                    newwo[k] = v
+            wo = newwo
 
         final_output_callback(wo, self.processStatus)
 

tests/fail-unconnected-expressiontool.cwl

@@ -0,0 +1,20 @@
+class: Workflow
+cwlVersion: v1.1
+inputs:
+  inp1:
+    type: string
+    default: hello inp1
+  inp2:
+    type: string
+    default: hello inp2
+outputs:
+  out:
+    type: string
+    outputSource: step1/out
+steps:
+  step1:
+    in:
+      in: inp1
+      in2: inp2
+    out: [out]
+    run: fail-unspecified-input-expressiontool.cwl

tests/fail-unspecified-input-expressiontool.cwl

@@ -0,0 +1,18 @@
+cwlVersion: v1.0
+class: ExpressionTool
+
+requirements:
+  InlineJavascriptRequirement: {} 
+
+inputs:
+  in:
+    type: string
+
+outputs:
+  out:
+    type: string
+
+expression: |
+  ${ 
+    return {"out": inputs.in +" "+inputs.in2};
+  }